I think I just found part of an answer. What few Rebels were left at Ft. Bliss as the California Column entered New Mexico in early/mid 1862 abandoned the post and Carlton actually used it as an outpost for most of the rest of the war. Still leaves open the question of who escorted the prisoners to San Antonio. Seems most likely it was the detatchment that was assigned to get them to El Paso area.

Putting two and two together, it appears that some prisoners may have still been in Santa Fe and others were picked up at Ft. Bliss (Franklin in Carlton's report.) Any/all comments welcome.